Molecule by Molecule
by PuzzlerthePony
Summary: Danny Phantom finally gets caught by his parents, but this time he can't escape.
1. Chapter 1

**This is my first fic here on Fanfiction. Enjoy! :)**

**Edited by Crazycoffeekat. Check out her stories! She's got a bunch of awesome DP, Chuck, and more!**

**Disclaimer: I do not own Danny Phantom.**

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**Molecule by Molecule**

Danny woke up slowly. He felt groggy- _really _groggy. "Ugh, what happened to me last night?" He thought, struggling to open his eyes.

For some odd reason, Danny couldn't quite remember what happened yesterday. His mind was very cloudy, and he simply assumed that he was tired and that he had slept in after a long night of ghost hunting. Figuring that was the case, Danny mentally shrugged it off.

"Mom probably has a stack of pancakes waiting for me." He smiled at the thought. "I better get downstairs."

With some hesitation, Danny started to roll his legs off his bed in a very clumsy manner.

His legs didn't move.

Danny's eyes shot wide open.

Danny tried again. This time he flung his legs as hard as he could-still no movement.

Panicking, he flailed his arms around, both of which were unusually resting over his head.

They didn't move.

"_Am I paralyzed_?"

Looking down at himself, Danny realized that he was in his black hazmat suit and white boots.

Crud. He was Danny Phantom.

Danny also noticed that he was in his parents lab on the examination table- restrained.

"Have... have I been caught again?" He wondered, flexing his sore muscles. "Gee, I must have been in the thermos all night!"

"HAH, escaping Mom and Dad will be way too easy!" Danny laughed to himself.

Grinning, Danny went intangible. "Sorry, Fentons!" He called out in a loud mock.

Danny went backwards through the examination table. The restraints around his limbs glowed, but they didn't give. Danny tried again to escape, floating upwards, and the

restraints that encircled his limbs brightened.

"_GAAAAH_!"

The sharp pain of electricity coursed throughout his entire body.

Danny slumped down in defeat, but he wouldn't give up yet; Danny still had one option left. Mustering up his remaining strength he lifted his torso up, allowing a white ring to form around his body.

"_Hrrgghh_!" Danny grunted, trying to revert back to his human form.

Almost instantaneously, another current of electricity shocked Danny, flowing through his body as if he were a wire. "_GAAAH_!" Danny screamed in pain.

He dropped back onto the examination table with a heavy thud. He was exhausted; all of his strength had been sapped out of him.

Danny tried to fight against the fatigue by keeping his head up. He struggling to remain conscious, but he was too weak. He couldn't stay awake any longer. Suddenly, his eyelids grew very heavy, and his head dropped down listlessly.

With one last, shuddering breath, Danny blacked out.

* * *

Danny awoke with a start.

Eyes flying open, he looked over himself. Crap. He was still trapped on the examination table, and still trapped in his ghost form.

"_JAZZ_!" Danny shouted. No answer "_MOM_! _DAD_!" Still nothing.

Fentonworks was deathly silent.

Turning his head towards the labratory's exit, Danny saw two silhouettes quietly stepping down the stairway.

"Mom. Dad..." Danny whispered under his breath.

Out of the stairway appeared the two notorious ghost hunters, Danny's parents, Jack and Maddie Fenton, who were— SMILING?

Walking up to Danny, they looked down at him and grinned maliciously. Danny looked up at his parents with pleading eyes, mentally begging them for his freedom.

"Hello, _ghost boy_." Maddie said, still smirking.

Well, this was awkward. "Uhh... Hi Mr. and Mrs. Fenton." Danny said with a big, fake smile.

"Do you like the new table?" Maddie asked. "It keeps ectoplasmic scum like you from going intangible, and it keeps them down by using their ecto-energy against them!" She finished, laughing excitedly.

"I call it the Fento-Specter-Trapper 12000!" Jack proudly declared, butting into the conversation.

Danny glared back. "What the heck do you want with me?"

"Oh, Phantom..." Maddie chided him. "For your crimes against Amnity park, we are going to lock you down here and examine your ectoplasmic body. _Molecule_," she whispered sadistically, "..._by molecule_."

Danny couldn't believe what he was hearing.

"I never committed any crimes!" He blurted out.

Of course, being framed by the mayor for aggravated assault and robbing the bank under the hypnotic control of Freakshow looked terrible, but Danny never meant for those accidents to happen. He had no control over any of those.

Danny dropped his head in guilt.

"Silence you... you ghost!" She spat the word out viciously.

"I'll leave him here for you, Maddie. You show that ghost!" Jack cheered.

"Meanwhile, Jazz and I will watch you tear him apart through the new Fentoncom video-feed I just installed!" Jack said, holding a small remote in his hand.

"Have fun Maddie!" He yelled as he pounded up the stairs with his remote, fully disappearing from Danny's sight.

Danny swallowed hard, his stomach dropping at the thought of watching his own body get ripped apart. And while he was awake, no less!

"Please," he begged. "Just let me go!"

"Sorry, Phantom," Maddie sneered, "but I just can't do that."

"I'll start preparing the needles." Maddie said as she switched back to her usual cheerful disposition, leaving Danny's sight to prepare for an array of invasive, inhumane experiments.

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**Reviews :D**


	2. Chapter 2

**Greetings fellow phans (and possibly a few haters)!**

**I have returned from the land of... umm, somewhere- maybe Narnia; the Ghost Zone? ****You get the picture.**

**I hope that this story stands out a little bit because I wanted to give Maddie a bit of a back-story and a more ulterior motive behind Danny's capture. **

**Thanks again Crazycoffeekat for beta-ing! You rock! **

**Be sure to check out her stories because I just blatantly product-placed her her, and shamelessly promoting another author is fun!**

**Disclaimer: I no own Danny Phantom.**

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Maddie Fenton thought back to her college days with Jack and Vlad. She remembered how the two young men had sparked her interest in the studies of the supernatural—ghosts especially.

Maddie remembered their first project together— the prototype ghost portal. It was after Vlad's accident with portal and her marriage with Jack that Maddie knew what she wanted to do for the rest of her life— she wanted to hunt and research ghosts to help the people around her.

Once Maddie had graduated college, she and Jack moved into a small apartment outside of Wisconsin so they could continue their studies on ghosts. It was a bit cramped and run-down, but to the newly wedded couple it was almost a dream house- they worked, researching, observing, experimenting, and finding relevance in almost anything 'supernatural' that they would discover.

Then Jazz and Danny came along. The births of her two children were the happiest days of Maddie's life. She knew that she was lucky to be blessed with two healthy, beautiful children. Although the new mother couldn't spend as much time in the lab as she used to, Maddie had been truly happy. And then things got tight.

Jack and Maddie's research came to a standstill. They barely had enough money to make it through the week, let alone feed Jazz and Danny. Maddie and Jack had to go hungry in order to spare food for their children. Before long, the landlord demanded that they vacate the apartment immediately.

At that point, Maddie's life seemed to crumble. Her entire world had shattered and broken. With the hunger and impoverishment, it seemed that life hated the Fentons.

On the night before the family was evicted, Maddie found a large envelope at her doorstep. She slowly read the return address and then read it over again.

Her eyes widened. _Impossible!_

She quickly opened it.

_From the Guys in White: Dear Mr. and Mrs. Fenton, our operatives are very interested in your research._

_ We would appreciate both of your aid in our research of ghosts and possibly their dimension, otherwise known as the Ghost Zone._

_ In addition, we would also require your assistance in the production of weapons to hunt, capture, and and deter ghosts. If you accept our offer, we will provide to you all necessary funding and tools, plus coverage for all personal expenses._

_ Thank you for your time and consideration._

_ Regards, The Guys in White. _

_1-369-742-6866_

"JACK!"

The Fenton family left their tiny apartment the next day, only to move into a house that was eight times its size. Each room was monumental, compared to sizes of the rooms in their previous living space. The kitchen was fully stocked, and the new Fenton laboratory was filled with an array of shiny gizmos and gadgets. Maddie beamed. Jazz and Danny could finally sleep in beds. It was a dream come true.

Things started looking up, and for the next decade, and the Fentons set to work; inventing, researching, selling, and cashing in. The Fenton's crowning achievement was the ghost portal, an interdimensional portal that could send people to the Ghost Zone. Although Jack and Maddie had no idea on how they got it to work, the two inventors felt very accomplished nonetheless. With their levels of ingenuity and intelligence, both Fenton children seemed to be following in Maddie's and Jack's footsteps.

Everything seemed to be perfect...

Until Danny started slipping away.

Maddie shrugged it off as a phase, but Danny became increasingly distant, and it seemed as if he had resigned from life itself. From the lies, to the dropping grades, to the blunt refusal of physical contact, Maddie knew that something was horribly wrong. Unfortunately, she couldn't be there for Danny when he needed her the most.

At that same time, Phantom showed up. The specter was nothing but trouble, causing hundreds of thousands of dollars in damage, flying around and catching her specimens, masquerading as a hero while everyone praised him... Phantom, of course, was no ordinary ghost. That much she knew. Everything about him disproved any and all of Maddie's theories. She'd already caught the ghost-boy biting into a Nasty Burger. The scientist couldn't deny how his face showed so much _emotion._ Maddie had seen Phantom laugh on many occasions. Although, only on one or two instances had she ever seen him cry.

Phantom, she'd realized, was an unsolvable mystery.

But she couldn't allow things to go on like this. _No!_ It was her duty to protect Amnity Park. So, Maddie threw herself into her work.

Consequently, she began to feel guilty and depressed over time for not giving enough emotional support to Danny, and she became very bitter towards herself. One day, while working in the lab, Maddie came to a sudden realization. The reason why she never had the time to help Danny, was because Phantom was always terrorizing the town that she needed to protect.

At this stark realization, the ghost hunter no longer felt guilty or frustrated. Instead, she turned those emotions into a fierce determination and anger. Maddie was consumed with the desire for revenge on the ghost who took up all of her time while her son was facing such an unstable stage in his life.

Maddie tightly held onto her grudge, where Phantom's capture became her own personal obsession. She vowed to get rid of that putrid piece of protoplasm and post-human consciousness.

Maddie Fenton was going to capture Danny Phantom once and for all.

Now, she had captured the ghost once, but he managed to escape again, and again, and again. This was infuriating, but Maddie learned from her mistakes, making sure that Phantom had his guard down when she was ready to strike. Maddie would hide in the the shadows like a hungry panther and watch her prey, noting his every move, his every flaw and weakness, and pounce when he would least suspect it. The mother constantly kept herself motivated by reminding herself that this was for Danny to make up for all of those moments that she lost.

On one night, all of Maddie's struggles and hard work finally payed off.

-o-MbM-o-

It was a warm, starry night. _"Danny would love to be outside right now._" Maddie murmured quietly to herself.

Phantom was flying in the middle of Amnity Park, slowly and gracefully in the sky. The gentle summer breeze caressed his silvery hair, which shined in the moonlight and added to his supernatural glow. The ghost-boy smiled softly to himself as he hummed a quiet tune, making loops and spinning amongst the stars as if they were his spotlights and he was the performer.

After an hour of keeping herself hidden, Maddie spotted Phantom, whose aura provided itself as a beacon of her target. The huntress carefully watched him from behind a tree. He seemed to be enjoying himself, and the ghost's care-free attitude sickened Maddie. Phantom stopped and hovered in midair, relaxing his arms behind his head and staring up at the stars; their soothing glow was like a quiet lullaby.

Phantom dozed off after a few minutes of floating in the same spot. Soon, his soft snores were the only audible noise in the entire park.

_Show time..._ Maddie slowly slunk out from her hiding place, her movements calculated and cat-like. Uncapping the Fenton thermos, she carefully aimed the opening at Phantom's body and pressed down on the side button.

_FWROOOSH!_

It was over in an instant.

_ Yes! I can't believe it— I finally captured Phantom!_

To say Maddie was overjoyed was a mere understatement. The scientist felt a sense of accomplishment and relief. Now Maddie could finally be there for Danny. Along with that, dissecting Phantom would uncover all sorts of new data.

_This could be the biggest moment of mine and Jack's career as ghost hunters!_ She'd set to work immediately.

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_ 'And all of my work has come down to this moment.'_ Maddie thought, turning to face her test subject for a moment. Maddie sighed, a small smile playing across her face.

Reaching inside a small cabinet, Maddie felt around until her hand landed on a familiar-feeling bottle.

_Perfect..._ The huntress thought, carefully opening the small vial. Soon, she filled two needles with the bottle's clear fluid.

Maddie searched a few more cabinets, pulling out sets of extremely sharp scalpels, needles, and other odds and ends that were obviously used for experimentation purposes. Figuring that she had enough supplies, Maddie wheeled her cart next to her test subject's experimentation table and set it in place.

Maddie towered over Phantom. The ghost had a terrified look in his toxic-green eyes, which glowed intensely with emotion. Phantom was still futilely pushing at his restraints. He—_no, it_, Maddie reminded herself—was also sweating profusely, his snow-white bangs slicking to his forehead.

Desperately, the half-ghost made one last attempt to break free and phased through the table again. The cuffs reacted instantaneously with their fluorescent green glow, and another electric shock racked through his body. _GAAAH!_ Phantom screamed in terror and agony, his body twitching and convulsing.

Maddie was unfazed. She turned her head back for a split second and smirked.

_Looks like the table's working just fine._ With the adrenaline coursing through his veins, Phantom wildly thrashed around, finding no escape from the horrible pain of electrocution. Lifting himself back up, Phantom dropped back on to the table with a heavy thud, returning himself to the tangible plane, and the pain immediately stopped.

Phantom's restraints dimmed, and his breathing was ragged and uneven. Phantom looked back up at Maddie with pleading eyes, begging for her mercy; begging for his freedom; begging for_ his life_.

Maddie didn't even so much as acknowledge this.

Using the Fento-Specter-Trapper 12000's control panel, the scientist elevated the table until her subject was laying three feet off of the ground so that it would be reachable. With a push of a button, Phantom was lifted upwards, meeting Maddie's feral gaze for a split second and then quickly turning away. Maddie noticed something else that was very, _very_ off with Phantom— he was _hyperventilating?_

_Well, I'll figure that what that means out soon enough. Time to get to work._

Phantom's heart beat heavily in his chest.

_There's no other option..._Phantom frantically thought, trembling in his bonds. _If I don't tell her my secret, I'll probably die._

Never had the ghost-boy felt seriously scared, especially for his own life. Doubts and fear clouded his mind. Phantom trembled violently as he sunk deeper and deeper into his thoughts.

Finding no better alternatives than revealing his half -ghost status, Phantom grew serious. _Whether or not she accepts me, it's still worth a shot. It's about time I told her anyway. Mom deserves to know, no matter what! Wait a minute...is that a video camera? What the heck, Mom? Seriously, You're going to try and videotape my death?_

Phantom wished he could have face-palmed himself right then and there.

The ghost saw Maddie coming closer. _This is my chance!_

She hovered directly over him.

Putting on a defeated face, Phantom looked straight into his mother's eyes. He took in a breath. "M-Maddie, um, I mean- Mrs. Fenton, I have something to tell you— something that I should have told you a _long_ time ago."

Maddie seemed to acknowledge this, yet her face was still blank, emotionless.

"About a year ago, I was in a... l-lab accident. I was electrocuted. It hurt pretty badly, but that wasn't all that happened..." Phantom quietly said.

Maddie made eye contact with him, and she softly stroked her hand on the back of his neck, through his ivory hair.

The ghost spoke up again a little louder. "I decided to fight ghosts, like you do. I've seen what you do, and I wanted to follow in your footsteps." His voice gradually grew louder." I wanted to protect the town from the bad ghosts. I wanted to be like you. I wanted to be a _hero._" Phantom finished, his voice reverberating fierce determination and pride.

Maddie kept rubbing the half-ghost's hair in-between her fingers.

_ JUST TELL HER ALREADY! _Phantom mentally screamed at himself.

He took a deep breath. "I'm not just a ghost. I'm Danny. I—_ Ow!_

The pinprick of a shot needle into his neck cut him off.

Maddie quickly injected the toxin.

The look in his mother's eyes said it all: she was truly disgusted with him. Half-ghost or not, he was the most horrible, repulsive being that ever existed, and Maddie would have rejected him either way.

It was hopeless.

She slowly removed the needle from his flesh with a satisfied smirk.

Phantom was flabbergasted. He turned his head towards her.

It wouldn't move.

The ghost-boy tried tried to move his arms and legs. They simply responded with faint twitches.

Soon, they didn't budge.

Danny Phantom opened his mouth one last time, struggling to form coherent words . With great effort, he gasped out his last sentence before his mouth and his body became completely still.

_''I love you, Mom...''_

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**Don't worry! Nothing was revealed! **

**Tell me what I'm doing right. Tell me what I'm doing wrong, because I like reviews! **

**We all do. Don't we?**

******Also, there is a hidden Easter egg in this chapter! Whoever found it gets this cookie (::)!**

**I hope you liked this chapter, because I'm already writing the third one!**

**:3**


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